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Jeong E, Kim V, Kim C, Lee YB, Kim D. Structural Insights into the Interaction of Terpenoids with Streptomyces avermitilis CYP107P2. Biomol Ther (Seoul) 2024; 32:474-480. [PMID: 38835149 PMCID: PMC11214959 DOI: 10.4062/biomolther.2024.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 06/06/2024] Open
Abstract
Streptomyces avermitilis genome includes 33 genes encoding monooxygenation-catalyzing cytochrome P450 enzymes. We investigated the structure of CYP107P2 and its interactions with terpenoid compounds. The recombinant CYP107P2 protein was expressed in Escherichia coli and the purified enzyme exhibited a typical P450 spectrum upon CO-binding in its reduced state. Type-I substrate-binding spectral titrations were observed with various terpenoid compounds, including α-pinene, β-pinene, α-terpinyl acetate, and (+)-3-carene. The calculated binding affinities (Kd) ranged from 15.9 to 50.8 μM. The X-ray crystal structure of CYP107P2 was determined at 1.99 Å resolution, with a well-conserved overall P450 folding conformation. The terpenoid compound docking models illustrated that the structural interaction between monoterpenes and CYP107P2, with the distance between heme and terpenes ranging from 3.4 to 5.4 Å, indicates potential substrate binding for P450 enzyme. This study suggests that CYP107P2 is a Streptomyces P450 enzyme capable of catalyzing terpenes as substrates, signifying noteworthy advancements in comprehending a novel P450 enzyme's involvement in terpene reactions.
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Affiliation(s)
- Eunseo Jeong
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Vitchan Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Changmin Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Yoo-bin Lee
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Donghak Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
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2
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Adhikari A, Shakya S, Shrestha S, Aryal D, Timalsina KP, Dhakal D, Khatri Y, Parajuli N. Biocatalytic role of cytochrome P450s to produce antibiotics: A review. Biotechnol Bioeng 2023; 120:3465-3492. [PMID: 37691185 DOI: 10.1002/bit.28548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/15/2023] [Accepted: 08/26/2023] [Indexed: 09/12/2023]
Abstract
Cytochrome P450s belong to a family of heme-binding monooxygenases, which catalyze regio- and stereospecific functionalisation of C-H, C-C, and C-N bonds, including heteroatom oxidation, oxidative C-C bond cleavages, and nitrene transfer. P450s are considered useful biocatalysts for the production of pharmaceutical products, fine chemicals, and bioremediating agents. Despite having tremendous biotechnological potential, being heme-monooxygenases, P450s require either autologous or heterologous redox partner(s) to perform chemical transformations. Randomly distributed P450s throughout a bacterial genome and devoid of particular redox partners in natural products biosynthetic gene clusters (BGCs) showed an extra challenge to reveal their pharmaceutical potential. However, continuous efforts have been made to understand their involvement in antibiotic biosynthesis and their modification, and this review focused on such BGCs. Here, particularly, we have discussed the role of P450s involved in the production of macrolides and aminocoumarin antibiotics, nonribosomal peptide (NRPSs) antibiotics, ribosomally synthesized and post-translationally modified peptide (RiPPs) antibiotics, and others. Several reactions catalyzed by P450s, as well as the role of their redox partners involved in the BGCs of various antibiotics and their derivatives, have been primarily addressed in this review, which would be useful in further exploration of P450s for the biosynthesis of new therapeutics.
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Affiliation(s)
- Anup Adhikari
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Sajan Shakya
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Shreesti Shrestha
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Dipa Aryal
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Kavi Prasad Timalsina
- Department of Biotechnology, National College, Tribhuvan University, Kathmandu, Nepal
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida, USA
| | | | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
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3
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Prestes ADS, Dos Santos MM, Kamdem JP, Mancini G, Schüler da Silva LC, de Bem AF, Barbosa NV. Methylglyoxal disrupts the functionality of rat liver mitochondria. Chem Biol Interact 2022; 351:109677. [PMID: 34634269 DOI: 10.1016/j.cbi.2021.109677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/10/2021] [Accepted: 09/29/2021] [Indexed: 11/15/2022]
Abstract
Methylglyoxal (MG) is a reactive metabolite derived from different physiological pathways. Its production can be harmful to cells via glycation reactions of lipids, DNA, and proteins. But, the effects of MG on mitochondrial functioning and bioenergetic responses are still elusive. Then, the effects of MG on key parameters of mitochondrial functionality were examined here. Isolated rat liver mitochondria were exposed to 0.1-10 mM of MG to determine its toxicity in the mitochondrial viability, membrane potential (Δψm), swelling and the superoxide (O2•-) production. Besides, mitochondrial oxidative phosphorylation parameters were analyzed by high-resolution respiratory (HRR) assay. In this set of experiments, routine state, PM state (pyruvate/malate), oxidative phosphorylation (OXPHOS), LEAK respiration, electron transport system (ETS) and oxygen residual (ROX) states were evaluated. HRR showed that PM state, OXPHOS CI-Linked, LEAK respiration, ETS CI/CII-Linked and ETS CII-Linked/ROX were significantly inhibited by MG exposure. MG also inhibited the complex II activity, and decreased Δψm and the viability of mitochondria. Taken together, our data indicates that MG is an inductor of mitochondrial dysfunctions and impairs important steps of respiratory chain, effects that can alter bioenergetics responses.
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Affiliation(s)
- Alessandro de Souza Prestes
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, Brazil.
| | - Matheus Mülling Dos Santos
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Jean Paul Kamdem
- Department of Biological Sciences, Regional University of Cariri, Pimenta, Crato, CE, Brazil
| | - Gianni Mancini
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | | | - Andreza Fabro de Bem
- Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Nilda Vargas Barbosa
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, Brazil
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4
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Kim V, Lim YR, Lee I, Lee JH, Han S, Pham TV, Kim H, Lee R, Kang LW, Kim D. Structural insights into CYP107G1 from rapamycin-producing Streptomyces rapamycinicus. Arch Biochem Biophys 2020; 692:108544. [PMID: 32822639 DOI: 10.1016/j.abb.2020.108544] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 10/23/2022]
Abstract
Rapamycin is a clinically important macrolide agent with immunosuppressant and antiproliferative properties, produced by the actinobacterium, Streptomyces rapamycinicus. Two cytochrome P450 enzymes are involved in the biosynthesis of rapamycin. CYP107G1 and CYP122A2 catalyze the oxidation reactions of C27 and C9 of pre-rapamycin, respectively. To understand the structural and biochemical features of P450 enzymes in rapamycin biosynthesis, the CYP107G1 and CYP122A2 genes were cloned, their recombinant proteins were expressed in Escherichia coli, and the purified enzymes were characterized. Both enzymes displayed low spin states in the absolute spectra of ferric forms, and the titrations with rapamycin induced type I spectral changes with Kd values of 4.4 ± 0.4 and 3.0 ± 0.3 μM for CYP107G1 and CYP122A2, respectively. The X-ray crystal structures of CYP107G1 and its co-crystal complex with everolimus, a clinical rapamycin derivative, were determined at resolutions of 2.9 and 3.0 Å, respectively. The overall structure of CYP107G1 adopts the canonical scaffold of cytochrome P450 and possesses large substrate pocket. The distal face of the heme group is exposed to solvents to accommodate macrolide access. When the structure of the everolimus-bound CYP107G1 complex (CYP107G1-Eve) was compared to that of the ligand-free CYP107G1 form, no significant conformational change was observed. Hence, CYP107G1 has a relatively rigid structure with versatile loops to accommodate a bulky substrate. The everolimus molecule is bound to the substrate-binding pocket in the shape of a squeezed donut, and its elongated structure is bound perpendicular to a planar heme plane and I-helix.
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Affiliation(s)
- Vitchan Kim
- Department of Biological Sciences, Konkuk University, Seoul, 05025, Republic of Korea
| | - Young-Ran Lim
- Department of Biological Sciences, Konkuk University, Seoul, 05025, Republic of Korea
| | - Inho Lee
- Department of Biological Sciences, Konkuk University, Seoul, 05025, Republic of Korea
| | - Jong-Ha Lee
- Department of Biological Sciences, Konkuk University, Seoul, 05025, Republic of Korea
| | - Sangjun Han
- Department of Biological Sciences, Konkuk University, Seoul, 05025, Republic of Korea
| | - Tan-Viet Pham
- Department of Biological Sciences, Konkuk University, Seoul, 05025, Republic of Korea
| | - Harim Kim
- Department of Biological Sciences, Konkuk University, Seoul, 05025, Republic of Korea
| | - Rowoon Lee
- Department of Biological Sciences, Konkuk University, Seoul, 05025, Republic of Korea
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul, 05025, Republic of Korea
| | - Donghak Kim
- Department of Biological Sciences, Konkuk University, Seoul, 05025, Republic of Korea.
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Mnguni FC, Padayachee T, Chen W, Gront D, Yu JH, Nelson DR, Syed K. More P450s Are Involved in Secondary Metabolite Biosynthesis in Streptomyces Compared to Bacillus, Cyanobacteria, and Mycobacterium. Int J Mol Sci 2020; 21:ijms21134814. [PMID: 32646068 PMCID: PMC7369989 DOI: 10.3390/ijms21134814] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 12/18/2022] Open
Abstract
Unraveling the role of cytochrome P450 monooxygenases (CYPs/P450s), heme-thiolate proteins present in living and non-living entities, in secondary metabolite synthesis is gaining momentum. In this direction, in this study, we analyzed the genomes of 203 Streptomyces species for P450s and unraveled their association with secondary metabolism. Our analyses revealed the presence of 5460 P450s, grouped into 253 families and 698 subfamilies. The CYP107 family was found to be conserved and highly populated in Streptomyces and Bacillus species, indicating its key role in the synthesis of secondary metabolites. Streptomyces species had a higher number of P450s than Bacillus and cyanobacterial species. The average number of secondary metabolite biosynthetic gene clusters (BGCs) and the number of P450s located in BGCs were higher in Streptomyces species than in Bacillus, mycobacterial, and cyanobacterial species, corroborating the superior capacity of Streptomyces species for generating diverse secondary metabolites. Functional analysis via data mining confirmed that many Streptomyces P450s are involved in the biosynthesis of secondary metabolites. This study was the first of its kind to conduct a comparative analysis of P450s in such a large number (203) of Streptomyces species, revealing the P450s’ association with secondary metabolite synthesis in Streptomyces species. Future studies should include the selection of Streptomyces species with a higher number of P450s and BGCs and explore the biotechnological value of secondary metabolites they produce.
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Affiliation(s)
- Fanele Cabangile Mnguni
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
| | - Wanping Chen
- Department of Molecular Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany;
| | - Dominik Gront
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Jae-Hyuk Yu
- Department of Bacteriology, University of Wisconsin-Madison, 3155 MSB, 1550 Linden Drive, Madison, WI 53706, USA;
- Department of Systems Biotechnology, Konkuk University, Seoul 05029, Korea
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Correspondence: (D.R.N.); (K.S.)
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (F.C.M.); (T.P.)
- Correspondence: (D.R.N.); (K.S.)
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6
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Cho MA, Han S, Lim YR, Kim V, Kim H, Kim D. Streptomyces Cytochrome P450 Enzymes and Their Roles in the Biosynthesis of Macrolide Therapeutic Agents. Biomol Ther (Seoul) 2019; 27:127-133. [PMID: 30562877 PMCID: PMC6430224 DOI: 10.4062/biomolther.2018.183] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/08/2018] [Accepted: 10/08/2018] [Indexed: 12/14/2022] Open
Abstract
The study of the genus Streptomyces is of particular interest because it produces a wide array of clinically important bioactive molecules. The genomic sequencing of many Streptomyces species has revealed unusually large numbers of cytochrome P450 genes, which are involved in the biosynthesis of secondary metabolites. Many macrolide biosynthetic pathways are catalyzed by a series of enzymes in gene clusters including polyketide and non-ribosomal peptide synthesis. In general, Streptomyces P450 enzymes accelerate the final, post-polyketide synthesis steps to enhance the structural architecture of macrolide chemistry. In this review, we discuss the major Streptomyces P450 enzymes research focused on the biosynthetic processing of macrolide therapeutic agents, with an emphasis on their biochemical mechanisms and structural insights.
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Affiliation(s)
- Myung-A Cho
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Songhee Han
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Young-Ran Lim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Vitchan Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Harim Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Donghak Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
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7
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IdeR, a DtxR Family Iron Response Regulator, Controls Iron Homeostasis, Morphological Differentiation, Secondary Metabolism, and the Oxidative Stress Response in Streptomyces avermitilis. Appl Environ Microbiol 2018; 84:AEM.01503-18. [PMID: 30194099 DOI: 10.1128/aem.01503-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/29/2018] [Indexed: 01/29/2023] Open
Abstract
Iron, an essential element for microorganisms, functions as a vital cofactor in a wide variety of key metabolic processes. On the other hand, excess iron may have toxic effects on bacteria by catalyzing the formation of reactive oxygen species through the Fenton reaction. The prevention of iron toxicity requires the precise control of intracellular iron levels in bacteria. Mechanisms of iron homeostasis in the genus Streptomyces (the producers of various antibiotics) are poorly understood. Streptomyces avermitilis is the industrial producer of avermectins, which are potent anthelmintic agents widely used in medicine, agriculture, and animal husbandry. We investigated the regulatory role of IdeR, a DtxR family regulator, in S. avermitilis In the presence of iron, IdeR binds to a specific palindromic consensus sequence in promoters and regulates 14 targets involved in iron metabolism (e.g., iron acquisition, iron storage, heme metabolism, and Fe-S assembly). IdeR also directly regulates 12 targets involved in other biological processes, including morphological differentiation, secondary metabolism, carbohydrate metabolism, and the tricarboxylic acid (TCA) cycle. ideR transcription is positively regulated by the peroxide-sensing transcriptional regulator OxyR. A newly constructed ideR deletion mutant (DideR) was found to be less responsive to iron levels and more sensitive to H2O2 treatment than the wild-type strain, indicating that ideR is essential for oxidative stress responses. Our findings, taken together, demonstrate that IdeR plays a pleiotropic role in the overall coordination of metabolism in Streptomyces spp. in response to iron levels.IMPORTANCE Iron is essential to almost all organisms, but in the presence of oxygen, iron is both poorly available and potentially toxic. Streptomyces species are predominantly present in soil where the environment is complex and fluctuating. So far, the mechanism of iron homeostasis in Streptomyces spp. remains to be elucidated. Here, we characterized the regulatory role of IdeR in the avermectin-producing organism S. avermitilis IdeR maintains intracellular iron levels by regulating genes involved in iron absorption and storage. IdeR also directly regulates morphological differentiation, secondary metabolism, and central metabolism. ideR is under the positive control of OxyR and is indispensable for an efficient response to oxidative stress. This investigation uncovered that IdeR acts as a global regulator coordinating iron homeostasis, morphological differentiation, secondary metabolism, and oxidative stress response in Streptomyces species. Elucidation of the pleiotropic regulation function of IdeR provides new insights into the mechanisms of how Streptomyces spp. adapt to the complex environment.
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8
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Choi YK. Role of Carbon Monoxide in Neurovascular Repair Processing. Biomol Ther (Seoul) 2018; 26:93-100. [PMID: 29223144 PMCID: PMC5839486 DOI: 10.4062/biomolther.2017.144] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/14/2017] [Accepted: 08/17/2017] [Indexed: 01/07/2023] Open
Abstract
Carbon monoxide (CO) is a gaseous molecule produced from heme by heme oxygenase (HO). Endogenous CO production occurring at low concentrations is thought to have several useful biological roles. In mammals, especially humans, a proper neurovascular unit comprising endothelial cells, pericytes, astrocytes, microglia, and neurons is essential for the homeostasis and survival of the central nervous system (CNS). In addition, the regeneration of neurovascular systems from neural stem cells and endothelial precursor cells after CNS diseases is responsible for functional repair. This review focused on the possible role of CO/HO in the neurovascular unit in terms of neurogenesis, angiogenesis, and synaptic plasticity, ultimately leading to behavioral changes in CNS diseases. CO/HO may also enhance cellular networks among endothelial cells, pericytes, astrocytes, and neural stem cells. This review highlights the therapeutic effects of CO/HO on CNS diseases involved in neurogenesis, synaptic plasticity, and angiogenesis. Moreover, the cellular mechanisms and interactions by which CO/HO are exploited for disease prevention and their therapeutic applications in traumatic brain injury, Alzheimer's disease, and stroke are also discussed.
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Affiliation(s)
- Yoon Kyung Choi
- Department of Integrative Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
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Rudolf JD, Chang CY, Ma M, Shen B. Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. Nat Prod Rep 2017; 34:1141-1172. [PMID: 28758170 PMCID: PMC5585785 DOI: 10.1039/c7np00034k] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to January 2017Cytochrome P450 enzymes (P450s) are some of the most exquisite and versatile biocatalysts found in nature. In addition to their well-known roles in steroid biosynthesis and drug metabolism in humans, P450s are key players in natural product biosynthetic pathways. Natural products, the most chemically and structurally diverse small molecules known, require an extensive collection of P450s to accept and functionalize their unique scaffolds. In this review, we survey the current catalytic landscape of P450s within the Streptomyces genus, one of the most prolific producers of natural products, and comprehensively summarize the functionally characterized P450s from Streptomyces. A sequence similarity network of >8500 P450s revealed insights into the sequence-function relationships of these oxygen-dependent metalloenzymes. Although only ∼2.4% and <0.4% of streptomycete P450s have been functionally and structurally characterized, respectively, the study of streptomycete P450s involved in the biosynthesis of natural products has revealed their diverse roles in nature, expanded their catalytic repertoire, created structural and mechanistic paradigms, and exposed their potential for biomedical and biotechnological applications. Continued study of these remarkable enzymes will undoubtedly expose their true complement of chemical and biological capabilities.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
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Lim YR, Han S, Kim JH, Park HG, Lee GY, Le TK, Yun CH, Kim D. Characterization of a Biflaviolin Synthase CYP158A3 from Streptomyces avermitilis and Its Role in the Biosynthesis of Secondary Metabolites. Biomol Ther (Seoul) 2017; 25:171-176. [PMID: 27956713 PMCID: PMC5340542 DOI: 10.4062/biomolther.2016.182] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/22/2016] [Accepted: 09/22/2016] [Indexed: 11/16/2022] Open
Abstract
Streptomyces avermitilis produces clinically useful drugs such as avermectins and oligomycins. Its genome contains approximately 33 cytochrome P450 genes and they seem to play important roles in the biosynthesis of many secondary metabolites. The SAV_7130 gene from S. avermitilis encodes CYP158A3. The amino acid sequence of this enzyme has high similarity with that of CYP158A2, a biflaviolin synthase from S. coelicolor A3(2). Recombinant S. avermitilis CYP158A3 was heterologously expressed and purified. It exhibited the typical P450 Soret peak at 447 nm in the reduced CO-bound form. Type I binding spectral changes were observed when CYP158A3 was titrated with myristic acid; however, no oxidative product was formed. An analog of flaviolin, 2-hydroxynaphthoquinone (2-OH NQ) displayed similar type I binding upon titration with purified CYP158A3. It underwent an enzymatic reaction forming dimerized product. A homology model of CYP158A3 was superimposed with the structure of CYP158A2, and the majority of structural elements aligned. These results suggest that CYP158A3 might be an orthologue of biflaviolin synthase, catalyzing C-C coupling reactions during pigment biosynthesis in S. avermitilis.
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Affiliation(s)
- Young-Ran Lim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Songhee Han
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Joo-Hwan Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Hyoung-Goo Park
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
| | - Ga-Young Lee
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Thien-Kim Le
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Chul-Ho Yun
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Donghak Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025, Republic of Korea
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11
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Han S, Pham TV, Kim JH, Lim YR, Park HG, Jeong D, Yun CH, Chun YJ, Kang LW, Kim D. Structural insights into the binding of lauric acid to CYP107L2 from Streptomyces avermitilis. Biochem Biophys Res Commun 2016; 482:902-908. [PMID: 27890614 DOI: 10.1016/j.bbrc.2016.11.131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 11/24/2016] [Indexed: 01/27/2023]
Abstract
Streptomyces avermitilis is an actinobacterium known to produce clinically useful macrolides including avermectins. CYP107L2 from S. avermitilis shares a high sequence similarity with the PikC (CYP107L1) from S. venezuelae. To elucidate the structural features of CYP107L2, we conducted biochemical and structural characterization of CYP107L2 from S. avermitilis. The CYP107L2 gene was cloned, and its recombinant protein was expressed and purified. The CYP107L2 showed a low-spin state of heme, and the reduced form yielded the CO difference spectra with a maximal absorption at 449 nm. Binding of pikromycin and lauric acid yielded the typical type I spectra with Kd values of 4.8 ± 0.3 and 111 ± 9 μM, respectively. However, no metabolic product was observed in the enzyme reaction. X-ray crystal structures of the ligand-free CYP107L2 and its complex with lauric acid were determined at the resolution of 2.6 and 2.5 Å, respectively. CYP107L2 showed a well-conserved CYP structure with a wide-open substrate-binding cavity. The lauric acid is bound mainly via hydrophobic interactions with the carboxylate group of lauric acid coordinated to the heme of P450. Glu-40 and Leu-382 residues in the CYP107L2 complex with lauric acid showed significant conformational changes to provide plentiful room for the lauric acid in the substrate-binding site.
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Affiliation(s)
- Songhee Han
- Department of Biological Sciences, Konkuk University, Seoul 05025 South Korea
| | - Tan-Viet Pham
- Department of Biological Sciences, Konkuk University, Seoul 05025 South Korea; Department of Biotechnology, Institute of Biotechnology and Food Technology, Industrial University of Ho Chi Minh City, Ho Chi Minh City, Viet Nam
| | - Joo-Hwan Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025 South Korea
| | - Young-Ran Lim
- Department of Biological Sciences, Konkuk University, Seoul 05025 South Korea
| | - Hyoung-Goo Park
- Department of Biological Sciences, Konkuk University, Seoul 05025 South Korea
| | - Dabin Jeong
- Department of Biological Sciences, Konkuk University, Seoul 05025 South Korea
| | - Chul-Ho Yun
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, South Korea
| | - Young-Jin Chun
- College of Pharmacy, Chung-Ang University, Seoul 06974, South Korea
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul 05025 South Korea.
| | - Donghak Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025 South Korea.
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12
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Guengerich FP, Waterman MR, Egli M. Recent Structural Insights into Cytochrome P450 Function. Trends Pharmacol Sci 2016; 37:625-640. [PMID: 27267697 PMCID: PMC4961565 DOI: 10.1016/j.tips.2016.05.006] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/07/2016] [Accepted: 05/11/2016] [Indexed: 02/08/2023]
Abstract
Cytochrome P450 (P450) enzymes are important in the metabolism of drugs, steroids, fat-soluble vitamins, carcinogens, pesticides, and many other types of chemicals. Their catalytic activities are important issues in areas such as drug-drug interactions and endocrine function. During the past 30 years, structures of P450s have been very helpful in understanding function, particularly the mammalian P450 structures available in the past 15 years. We review recent activity in this area, focusing on the past 2 years (2014-2015). Structural work with microbial P450s includes studies related to the biosynthesis of natural products and the use of parasitic and fungal P450 structures as targets for drug discovery. Studies on mammalian P450s include the utilization of information about 'drug-metabolizing' P450s to improve drug development and also to understand the molecular bases of endocrine dysfunction.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.
| | - Michael R Waterman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.
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